See You at ASHG — Lunch Is on Us!

We are looking forward to catching up with you at ASHG. You can stop by booth #915 to check out the latest and get a demo of DNAnexus, or join our lunch workshop on Wednesday to hear about a massive-scale genomic study that performed its analysis in our cloud environment.

Jeffrey Reid HGSCAt the workshop, you’ll hear from Jeffrey Reid, assistant professor at the Baylor College of Medicine’s Human Genome Sequencing Center (HGSC), who will talk about his experience using our computing solution for the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium, a group of more than 300 scientists. Dr. Reid will discuss the technical and practical challenges related to the analysis of over 14,000 genomes or exomes, such as meeting peak compute demand, enabling secure access for multiple researchers and sharing tools and results across the entire consortium.

At the project’s peak, HGSC was able to spin up over 20,000 AWS cores on-demand in order to run the analysis pipeline of the CHARGE data. During this period, HGSC was running one of the largest genomics analysis clusters in the world!

We’ll also be hosting a CHARGE Q&A Hour at our booth (#915) on Thursday, October 24th, from 11am to noon. Stop by if you’d like to learn more about the CHARGE project; folks from the HGSC and DNAnexus will be on hand to answer any questions.

Workshop details

• Wednesday, October 23rd, 12:30 – 2:00 pm
• Room 209, Level 2, Convention Center
• Boxed lunch & refreshments will be provided

Agenda

Realizing the Full Potential of Mega-Scale Cohort Analysis in the Cloud

Introduction
Andreas Sundquist, PhD, CTO & Co-founder, DNAnexus

The Nuts & Bolts of Enabling Ultra Large-Scale Genomic Analysis in the Cloud
Andrew Carroll, PhD, Scientist, DNAnexus

Vacation Slides from Bespin: A Guided Tour Through Large-Scale Genomic Analysis in the Cloud
Jeffrey Reid, PhD, Research Assistant Professor, BCM Human Genome Sequencing Center

ASHG: With Great Science Comes Great Responsibility

ASHG Conference 2012The American Society of Human Genetics annual meeting was held at the Moscone Center in San Francisco, not far from DNAnexus headquarters in Mountain View, Calif. Several of us were lucky enough to make the short trip and check out what is widely considered the biggest genomics conference of the year, this time with almost 7,000 scientists in attendance.

The conference kicked off with a plenary talk from the University of Washington’s Mary-Claire King, 2012 President of ASHG. Her focus, “The Scientist as a Citizen of the World,” really resonated with attendees — as evidenced not only by the energy in the room, but by how many people were tweeting from King’s address. She told attendees that scientists have a responsibility to put their knowledge and common sense to use, not just in the lab but as world citizens. She also urged researchers to remember that no question is too large or too daunting to be asked.

Another session that really stirred interest centered on gene patents. Panelists, including Mark Lemley from Stanford and Lori Andrews from the Hastings Institute, discussed the Myriad BRCA gene patents in depth, adding context from other cases, such as Prometheus and a GlaxoSmithKline patent related to asthma. Regardless of your view on the patentability of genes, this was a fascinating discussion that highlighted the importance — both in the commercial market and in academic research — of linking genes to particular traits.

The ASHG meeting is known as the place to give out major genetics awards, and this year’s event did not disappoint. Some leading names in the field went home with new recognition, including: Uta Francke, formerly at Stanford and now Senior Medical Director at 23&Me (ASHG William Allan Award); Jay Shendure at the University of Washington (ASHG Curt Stern Award); Alan Emery of the University of Edinburgh (ASHG Award for Excellence in Human Genetics Education); and Douglas Wallace at the Children’s Hospital of Philadelphia (Gruber Genetics Prize).

One award winner offered a particularly popular talk: NIH Director Francis Collins was on site to give the ASHG Victor A. McKusick Leadership Award Presentation. Collins, a longtime ASHG champion, bemoaned the state of funding for life sciences, noting that his agency’s budget is now 20 percent lower in constant dollars than it was in 2003. He encouraged scientists to promote the value of research in their communities, helping the public understand why it is so important to continue strong funding levels for scientific research.

We were proud to be active participants at ASHG, with our exhibit hall booth and our luncheon workshop featuring a customer story from Anshul Kundaje, presenting his latest Encode paper, along with the latest information about DNAnexus from our CEO Andreas Sundquist. It was an honor to have so many attendees take part in our workshop — thanks to everyone for taking the time to learn more about DNAnexus.

We raffled off an iPod to one of our luncheon or booth visitors, and the winner was Suleyman Gulsuner from the University of Washington. Congratulations, Suleyman!

A lot of what we learned at ASHG this year was related to responsibility: our collective responsibility to promote science and the scientific approach in the world, as well as the responsibility for enabling research with or without gene patents. At DNAnexus, our responsibility is to provide an easy-to-use, secure, and convenient platform to facilitate research and to help scientists make connections that are important enough to share with the broader world. We consider it a privilege to be entrusted with your data, and we take that responsibility very seriously.

Join DNAnexus for a Lunchtime Workshop at ASHG

Whether you join us for lunch to explore the dark matter of ENCODE or visit our booth (#507) to check out the latest updates and get a demo of DNAnexus, we’d love to catch up with you at ASHG. Plus, be entered to win an iPod Shuffle, when introducing yourself at the DNAnexus booth.

 

kundaje encodeWe are honored to have Dr. Anshul Kundaje, research scientist at MIT, review his latest ENCODE consortium paper and share insights into gene regulation. By looking at 119 transcription factors and regulatory proteins, Kundaje’s team found that chromatin diversity at the regulatory level is the norm, rather than the exception.

 

During this lunchtime talk you’ll discover how Kundaje and team used DNAnexus to process and map some 5 billion reads and identified chromatin patterns via a newly developed probabilistic mapping tool, the Clustered AGgregation Tool (CAGT). The clustering approach yielded dramatically different results compared to the standard method of averaging chromatin marks across populations. Importantly, Kundaje’s team was able to identify about 25 “metapatterns,” or signatures that represent the diversity of modifications across binding sites and cell types. These distinct patterns will be valuable for other scientists examining chromatin modifications and making inferences about what those changes are doing in the genome.

 

Details

• Wednesday, November 7th, 12:45 – 2:15 pm
• Moscone Center, Room 301 (Esplanade Level)
• Boxed lunch & refreshments will be provided!

 

Agenda

Introduction
Brigitte Ganter, Ph.D., Director of Product Marketing, DNAnexus

Ubiquitous Heterogeneity and Asymmetry of the Chromatin Environment at Human Regulatory Elements
Anshul Kundaje, Ph.D., Research Scientist MIT

DNAnexus: A Collaborative and Scalable Data Technology Platform
Andreas Sundquist, Ph.D., CEO and Co-founder, DNAnexus

 

Explore the data yourself; you’ll find the 20 samples accessible via DNAnexus in our Public Data folder, labeled Encode.